Recent applications of boxed molecular dynamics: a simple multiscale technique for atomistic simulations.
Recent applications of boxed molecular dynamics: a simple multiscale technique for atomistic simulations.
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DOI：
10.1098/rsta.2013.0384
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发表时间：
2014-08-06
期刊：
影响因子：
--
通讯作者：
Shalashilin DV
中科院分区：
文献类型：
--
作者：
Booth J;Vazquez S;Martinez-Nunez E;Marks A;Rodgers J;Glowacki DR;Shalashilin DV
本文简要介绍了用于复杂分子体系热力学和动力学分析的盒装分子动力学方法。BXD是一种多尺度技术，其中热力学和长时间动力学从一组短时间模拟中恢复。本文综述了BXD在多肽环化反应、溶液相有机反应动力学和离子自组装膜脱附等方面的应用。我们还报告了在原子力显微镜实验中模拟金刚石蚀刻机制和蛋白质展开的初步结果。后者表明蛋白质的结构基序和其潜在的平均力之间的相关性。用标准分子动力学（MD）模拟这些过程通常是不可能的，因为实验时间尺度非常长。然而，BXD产生良好收敛和物理上有意义的结果。与其他方法相比，加速MD，我们的BXD方法是非常简单的，它是易于实现的，它提供了一个综合的方法，同时获得热力学和动力学。它还提供了一个战略，获得统计上有意义的动态结果的配置空间，标准的MD方法将访问只有很少的区域。
In this paper, we briefly review the boxed molecular dynamics (BXD) method which allows analysis of thermodynamics and kinetics in complicated molecular systems. BXD is a multiscale technique, in which thermodynamics and long-time dynamics are recovered from a set of short-time simulations. In this paper, we review previous applications of BXD to peptide cyclization, solution phase organic reaction dynamics and desorption of ions from self-assembled monolayers (SAMs). We also report preliminary results of simulations of diamond etching mechanisms and protein unfolding in atomic force microscopy experiments. The latter demonstrate a correlation between the protein's structural motifs and its potential of mean force. Simulations of these processes by standard molecular dynamics (MD) is typically not possible, because the experimental time scales are very long. However, BXD yields well-converged and physically meaningful results. Compared with other methods of accelerated MD, our BXD approach is very simple; it is easy to implement, and it provides an integrated approach for simultaneously obtaining both thermodynamics and kinetics. It also provides a strategy for obtaining statistically meaningful dynamical results in regions of configuration space that standard MD approaches would visit only very rarely.
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影响因子：
2.8
作者：
Metzler, R;Klafter, J;Volk, M
通讯作者：
Volk, M
DOI：
10.1073/pnas.1211764109
发表时间：
2012-11-27
影响因子：
11.1
作者：
Milanesi, Lilia;Waltho, Jonathan P.;Volk, Martin
通讯作者：
Volk, Martin
影响因子：
4.4
作者：
Glowacki, David R.;Orr-Ewing, Andrew J.;Harvey, Jeremy N.
通讯作者：
Harvey, Jeremy N.
影响因子：
4.4
作者：
Guo, Y;Shalashilin, DV;Thompson, DL
通讯作者：
Thompson, DL
影响因子：
1.7
作者：
Glowacki, David R.;Lightfoot, Robert;Harvey, Jeremy N.
通讯作者：
Harvey, Jeremy N.